| 226 |
|
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
| 227 |
|
|
| 228 |
|
if (molInfo.nBonds > 0) |
| 229 |
< |
molInfo.myBonds = new (Bond *) [molInfo.nBonds]; |
| 229 |
> |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
| 230 |
|
else |
| 231 |
|
molInfo.myBonds = NULL; |
| 232 |
|
|
| 233 |
|
if (molInfo.nBends > 0) |
| 234 |
< |
molInfo.myBends = new (Bend *) [molInfo.nBends]; |
| 234 |
> |
molInfo.myBends = new Bend*[molInfo.nBends]; |
| 235 |
|
else |
| 236 |
|
molInfo.myBends = NULL; |
| 237 |
|
|
| 238 |
|
if (molInfo.nTorsions > 0) |
| 239 |
< |
molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions]; |
| 239 |
> |
molInfo.myTorsions = new Torsion *[molInfo.nTorsions]; |
| 240 |
|
else |
| 241 |
|
molInfo.myTorsions = NULL; |
| 242 |
|
|
| 948 |
|
|
| 949 |
|
info[i].useInitXSstate = globals->getUseInitXSstate(); |
| 950 |
|
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
| 951 |
< |
|
| 951 |
> |
|
| 952 |
> |
// check for thermodynamic integration |
| 953 |
> |
if (globals->getUseThermInt()) { |
| 954 |
> |
if (globals->haveThermIntLambda() && globals->haveThermIntK()) { |
| 955 |
> |
info[i].useThermInt = globals->getUseThermInt(); |
| 956 |
> |
info[i].thermIntLambda = globals->getThermIntLambda(); |
| 957 |
> |
info[i].thermIntK = globals->getThermIntK(); |
| 958 |
> |
|
| 959 |
> |
Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK); |
| 960 |
> |
info[i].restraint = myRestraint; |
| 961 |
> |
} |
| 962 |
> |
else { |
| 963 |
> |
sprintf(painCave.errMsg, |
| 964 |
> |
"SimSetup Error:\n" |
| 965 |
> |
"\tKeyword useThermInt was set to 'true' but\n" |
| 966 |
> |
"\tthermodynamicIntegrationLambda (and/or\n" |
| 967 |
> |
"\tthermodynamicIntegrationK) was not specified.\n" |
| 968 |
> |
"\tPlease provide a lambda value and k value in your .bass file.\n"); |
| 969 |
> |
painCave.isFatal = 1; |
| 970 |
> |
simError(); |
| 971 |
> |
} |
| 972 |
> |
} |
| 973 |
> |
else if(globals->haveThermIntLambda() || globals->haveThermIntK()){ |
| 974 |
> |
sprintf(painCave.errMsg, |
| 975 |
> |
"SimSetup Warning: If you want to use Thermodynamic\n" |
| 976 |
> |
"\tIntegration, set useThermInt to 'true' in your .bass file.\n" |
| 977 |
> |
"\tThe useThermInt keyword is 'false' by default, so your\n" |
| 978 |
> |
"\tlambda and/or k values are being ignored.\n"); |
| 979 |
> |
painCave.isFatal = 0; |
| 980 |
> |
simError(); |
| 981 |
> |
} |
| 982 |
|
} |
| 983 |
|
|
| 984 |
|
//setup seed for random number generator |
| 1288 |
|
} |
| 1289 |
|
else{ |
| 1290 |
|
strcat(info[k].statusName, ".stat"); |
| 1291 |
+ |
} |
| 1292 |
+ |
} |
| 1293 |
+ |
|
| 1294 |
+ |
strcpy(info[k].rawPotName, inFileName); |
| 1295 |
+ |
nameLength = strlen(info[k].rawPotName); |
| 1296 |
+ |
endTest = &(info[k].rawPotName[nameLength - 5]); |
| 1297 |
+ |
if (!strcmp(endTest, ".bass")){ |
| 1298 |
+ |
strcpy(endTest, ".raw"); |
| 1299 |
+ |
} |
| 1300 |
+ |
else if (!strcmp(endTest, ".BASS")){ |
| 1301 |
+ |
strcpy(endTest, ".raw"); |
| 1302 |
+ |
} |
| 1303 |
+ |
else{ |
| 1304 |
+ |
endTest = &(info[k].rawPotName[nameLength - 4]); |
| 1305 |
+ |
if (!strcmp(endTest, ".bss")){ |
| 1306 |
+ |
strcpy(endTest, ".raw"); |
| 1307 |
+ |
} |
| 1308 |
+ |
else if (!strcmp(endTest, ".mdl")){ |
| 1309 |
+ |
strcpy(endTest, ".raw"); |
| 1310 |
+ |
} |
| 1311 |
+ |
else{ |
| 1312 |
+ |
strcat(info[k].rawPotName, ".raw"); |
| 1313 |
|
} |
| 1314 |
|
} |
| 1315 |
|
|
| 1531 |
|
} |
| 1532 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
| 1533 |
|
|
| 1534 |
< |
info[0].n_atoms = mpiSim->getMyNlocal(); |
| 1534 |
> |
info[0].n_atoms = mpiSim->getLocalNatoms(); |
| 1535 |
|
|
| 1536 |
|
|
| 1537 |
|
if (local_atoms != info[0].n_atoms){ |
